A chemiluminescence method with potassium permanganate was developed for use as an indicator of organic pollutants in fresh water. This method could be applied to the determination of organic pollutants in seawater as well. However, the flow chemiluminescence method suffered from the interference of chloride ions at the same concentration of seawater because of the production of manganese dioxide in the oxidation of chloride ions with permanganate. The conditions (concentrations of potassium permanganate and sulfuric acid and sample volume, i.e. flow injection method) were chosen to minimize the interference of chloride ions. The chemiluminescence method shows a good correlation with the chemical oxygen demand method on fresh water added artificial sea salt and seawater samples. Natural seawater was analyzed by the chemiluminescence method. The results obtained were compared with those obtained by chemical oxygen demand under the alkaline condition and total organic carbon methods. The chemiluminescence method has higher sensitivity and reproducibility than the conventional chemical oxygen demand and total organic carbon methods.